/// <summary> /// constructor /// </summary> private CacheFile(string path, ushort refIndex, TranscriptDataSource ds, MiniCacheType type, IUpdater updater) { CachePath = path; TranscriptDataSource = ds; Type = type; ReferenceIndex = refIndex; Updater = updater; AddInputFiles(FileOperations.GetFullPathWithoutExtension(path)); }
private static CacheFile TryMatchFilename(string ndbPath, Func <string, Match> matcher, MiniCacheType type, ChromosomeRenamer renamer) { string filename = Path.GetFileName(ndbPath); if (filename == null) { return(null); } var match = matcher(filename); if (!match.Success) { return(null); } IUpdater updater; string id, transcriptDataSource; int position; ushort refIndex; switch (type) { case MiniCacheType.Transcript: var tuple = FormatUtilities.SplitVersion(match.Groups[1].Value); id = tuple.Item1; refIndex = renamer.GetReferenceIndex(match.Groups[2].Value); transcriptDataSource = match.Groups[3].Value; updater = new TranscriptUpdater(id, refIndex, transcriptDataSource); break; case MiniCacheType.Regulatory: id = match.Groups[1].Value; refIndex = renamer.GetReferenceIndex(match.Groups[2].Value); transcriptDataSource = match.Groups[3].Value; updater = new RegulatoryUpdater(id, refIndex, transcriptDataSource); break; case MiniCacheType.Position: refIndex = renamer.GetReferenceIndex(match.Groups[1].Value); position = int.Parse(match.Groups[2].Value); string refAllele = match.Groups[3].Value; string altAllele = match.Groups[4].Value; transcriptDataSource = match.Groups[5].Value; updater = new PositionUpdater(refIndex, position, refAllele, altAllele, transcriptDataSource); break; case MiniCacheType.PositionRange: refIndex = renamer.GetReferenceIndex(match.Groups[1].Value); position = int.Parse(match.Groups[2].Value); int endPosition = int.Parse(match.Groups[3].Value); transcriptDataSource = match.Groups[4].Value; updater = new PositionRangeUpdater(refIndex, position, endPosition, transcriptDataSource); break; default: throw new GeneralException($"Unexpected mini-cache type encountered: {type}"); } return(new CacheFile(ndbPath, updater.RefIndex, ConvertTranscriptDataSource(updater.TranscriptDataSource), type, updater)); }